Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3962L

Calculation Name: 1AZZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AZZ

Chain ID: A

ChEMBL ID:

UniProt ID: P00771

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2541498.31535
FMO2-HF: Nuclear repulsion 2457962.452566
FMO2-HF: Total energy -83535.862784
FMO2-MP2: Total energy -83776.683951


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:16:ILE)


Summations of interaction energy for fragment #1(A:16:ILE)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-33.467-15.42823.118-12.611-28.539-0.111
Interaction energy analysis for fragmet #1(A:16:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.020
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A18GLY00.0340.0123.691-0.3231.2870.006-0.698-0.9180.002
4A19GLY00.0100.0102.851-0.3820.1020.109-0.180-0.4130.001
5A20VAL0-0.097-0.0383.792-0.106-0.022-0.0020.042-0.1250.000
6A21GLU-1-0.848-0.9184.8841.5241.613-0.001-0.003-0.0840.000
7A22ALA00.0070.0056.507-0.266-0.2660.0000.0000.0000.000
8A23VAL00.006-0.0068.171-0.069-0.0690.0000.0000.0000.000
9A24PRO00.0640.03411.369-0.019-0.0190.0000.0000.0000.000
10A25ASN0-0.006-0.01812.343-0.054-0.0540.0000.0000.0000.000
11A26SER0-0.094-0.05710.880-0.045-0.0450.0000.0000.0000.000
12A27TRP0-0.005-0.0057.697-0.119-0.1190.0000.0000.0000.000
13A28PRO00.0300.01810.794-0.021-0.0210.0000.0000.0000.000
14A29HIS0-0.0040.0099.718-0.001-0.0010.0000.0000.0000.000
15A30GLN0-0.030-0.0026.308-0.080-0.0800.0000.0000.0000.000
16A31ALA00.0150.01010.1500.0490.0490.0000.0000.0000.000
17A32ALA00.0000.0079.619-0.088-0.0880.0000.0000.0000.000
18A33LEU0-0.020-0.01411.0310.0520.0520.0000.0000.0000.000
19A34PHE00.0310.01213.001-0.064-0.0640.0000.0000.0000.000
20A35ILE0-0.012-0.00714.5500.0190.0190.0000.0000.0000.000
21A37ASP-1-0.764-0.88417.317-0.138-0.1380.0000.0000.0000.000
22A38ASP-1-0.933-0.97018.956-0.059-0.0590.0000.0000.0000.000
23A39MET0-0.122-0.05118.0310.0050.0050.0000.0000.0000.000
24A40TYR0-0.039-0.02514.238-0.030-0.0300.0000.0000.0000.000
25A41PHE0-0.007-0.0017.1600.0630.0630.0000.0000.0000.000
26A42CYS0-0.111-0.0419.344-0.194-0.1940.0000.0000.0000.000
27A43GLY00.0630.0357.4730.0940.0940.0000.0000.0000.000
28A44GLY00.0410.0118.5130.0130.0130.0000.0000.0000.000
29A45SER0-0.052-0.0169.8110.0480.0480.0000.0000.0000.000
30A46LEU0-0.0230.00612.002-0.008-0.0080.0000.0000.0000.000
31A47ILE00.008-0.00815.2990.0140.0140.0000.0000.0000.000
32A48SER0-0.003-0.01517.6040.0080.0080.0000.0000.0000.000
33A49PRO00.0410.00520.321-0.004-0.0040.0000.0000.0000.000
34A50GLU-1-0.838-0.88122.463-0.018-0.0180.0000.0000.0000.000
35A51TRP00.0090.01220.089-0.007-0.0070.0000.0000.0000.000
36A52ILE00.0120.00814.0270.0120.0120.0000.0000.0000.000
37A53LEU00.0030.00713.379-0.007-0.0070.0000.0000.0000.000
38A54THR00.032-0.00211.312-0.027-0.0270.0000.0000.0000.000
39A55ALA00.0480.02411.3510.0260.0260.0000.0000.0000.000
40A56ALA0-0.0100.00113.2090.0060.0060.0000.0000.0000.000
41A57HIS10.8230.88011.2350.5260.5260.0000.0000.0000.000
42A59MET0-0.017-0.00814.8310.0330.0330.0000.0000.0000.000
43A60ASP-1-0.903-0.93418.193-0.176-0.1760.0000.0000.0000.000
44A61GLY00.0010.00220.6780.0170.0170.0000.0000.0000.000
45A61ALA0-0.050-0.00919.6790.0050.0050.0000.0000.0000.000
46A61GLY0-0.048-0.02921.8270.0120.0120.0000.0000.0000.000
47A62PHE0-0.100-0.05721.4760.0100.0100.0000.0000.0000.000
48A63VAL00.0310.00816.721-0.019-0.0190.0000.0000.0000.000
49A64ASP-1-0.830-0.90518.637-0.016-0.0160.0000.0000.0000.000
50A65VAL0-0.021-0.00515.008-0.014-0.0140.0000.0000.0000.000
51A66VAL0-0.008-0.00413.8640.0210.0210.0000.0000.0000.000
52A68LEU0-0.012-0.01713.940-0.013-0.0130.0000.0000.0000.000
53A69GLY00.0480.02014.9310.0060.0060.0000.0000.0000.000
54A70ALA0-0.0010.01212.2320.0000.0000.0000.0000.0000.000
55A71HIS0-0.095-0.0669.289-0.021-0.0210.0000.0000.0000.000
56A72ASN00.025-0.01910.4180.1820.1820.0000.0000.0000.000
57A73ILE00.0010.0099.338-0.117-0.1170.0000.0000.0000.000
58A74ARG10.8200.91910.275-0.339-0.3390.0000.0000.0000.000
59A75GLU-1-0.958-0.96815.1860.3310.3310.0000.0000.0000.000
60A76ASP-1-0.930-0.95917.5440.1230.1230.0000.0000.0000.000
61A77GLU-1-0.776-0.86215.0120.3890.3890.0000.0000.0000.000
62A78ALA0-0.026-0.02919.325-0.017-0.0170.0000.0000.0000.000
63A79THR0-0.084-0.05217.140-0.009-0.0090.0000.0000.0000.000
64A80GLN0-0.056-0.02715.552-0.042-0.0420.0000.0000.0000.000
65A81VAL0-0.042-0.01918.265-0.016-0.0160.0000.0000.0000.000
66A82THR00.0210.01018.2560.0020.0020.0000.0000.0000.000
67A83ILE0-0.073-0.03719.6810.0020.0020.0000.0000.0000.000
68A84GLN0-0.026-0.01220.499-0.010-0.0100.0000.0000.0000.000
69A85SER0-0.046-0.04921.2180.0070.0070.0000.0000.0000.000
70A86THR00.000-0.01122.618-0.007-0.0070.0000.0000.0000.000
71A87ASP-1-0.955-0.96123.704-0.058-0.0580.0000.0000.0000.000
72A88PHE00.033-0.00220.235-0.003-0.0030.0000.0000.0000.000
73A89THR0-0.043-0.00121.5010.0010.0010.0000.0000.0000.000
74A90VAL00.0190.01019.261-0.011-0.0110.0000.0000.0000.000
75A91HIS00.0340.01320.3100.0120.0120.0000.0000.0000.000
76A92GLU-1-0.812-0.89722.176-0.097-0.0970.0000.0000.0000.000
77A93ASN0-0.073-0.03824.5940.0050.0050.0000.0000.0000.000
78A94TYR0-0.036-0.02918.138-0.014-0.0140.0000.0000.0000.000
79A95ASN0-0.032-0.01421.5430.0050.0050.0000.0000.0000.000
80A96SER00.0580.02620.310-0.007-0.0070.0000.0000.0000.000
81A97PHE0-0.087-0.03720.793-0.014-0.0140.0000.0000.0000.000
82A98VAL0-0.036-0.02821.3830.0000.0000.0000.0000.0000.000
83A99ILE00.0160.02015.082-0.005-0.0050.0000.0000.0000.000
84A100SER00.0390.03217.592-0.003-0.0030.0000.0000.0000.000
85A101ASN0-0.047-0.06319.3920.0040.0040.0000.0000.0000.000
86A102ASP-1-0.703-0.79113.788-0.349-0.3490.0000.0000.0000.000
87A103ILE0-0.060-0.01214.673-0.027-0.0270.0000.0000.0000.000
88A104ALA00.016-0.00115.8190.0140.0140.0000.0000.0000.000
89A105VAL0-0.043-0.01116.343-0.005-0.0050.0000.0000.0000.000
90A106ILE00.0420.01615.7310.0010.0010.0000.0000.0000.000
91A107ARG10.8480.91519.4890.0420.0420.0000.0000.0000.000
92A108LEU0-0.021-0.00718.855-0.002-0.0020.0000.0000.0000.000
93A109PRO0-0.010-0.01522.8310.0040.0040.0000.0000.0000.000
94A110VAL0-0.029-0.01525.6500.0030.0030.0000.0000.0000.000
95A111PRO0-0.035-0.01124.9740.0010.0010.0000.0000.0000.000
96A112VAL00.0300.01820.9350.0060.0060.0000.0000.0000.000
97A113THR0-0.052-0.03923.8610.0000.0000.0000.0000.0000.000
98A114LEU00.0140.01620.9190.0060.0060.0000.0000.0000.000
99A115THR0-0.039-0.02820.6010.0060.0060.0000.0000.0000.000
100A116ALA0-0.043-0.03120.1240.0000.0000.0000.0000.0000.000
101A117ALA00.0080.01516.5050.0170.0170.0000.0000.0000.000
102A118ILE00.0040.01615.8770.0060.0060.0000.0000.0000.000
103A119ALA00.002-0.00816.615-0.012-0.0120.0000.0000.0000.000
104A120THR00.0100.01516.520-0.006-0.0060.0000.0000.0000.000
105A121VAL0-0.0250.00112.5240.0150.0150.0000.0000.0000.000
106A122GLY0-0.022-0.00615.593-0.013-0.0130.0000.0000.0000.000
107A123LEU00.0540.01316.087-0.007-0.0070.0000.0000.0000.000
108A124PRO00.0060.00316.1320.0090.0090.0000.0000.0000.000
109A125SER00.003-0.00419.025-0.006-0.0060.0000.0000.0000.000
110A127THR0-0.053-0.03321.095-0.003-0.0030.0000.0000.0000.000
111A128ASP-1-0.764-0.84017.939-0.071-0.0710.0000.0000.0000.000
112A129VAL0-0.023-0.00415.1010.0100.0100.0000.0000.0000.000
113A130GLY0-0.0100.00517.762-0.010-0.0100.0000.0000.0000.000
114A132VAL00.0320.02217.2730.0040.0040.0000.0000.0000.000
115A133GLY0-0.025-0.00616.5090.0080.0080.0000.0000.0000.000
116A134THR0-0.078-0.05814.2770.0170.0170.0000.0000.0000.000
117A135VAL0-0.0260.00010.563-0.015-0.0150.0000.0000.0000.000
118A136VAL0-0.026-0.0158.4910.0050.0050.0000.0000.0000.000
119A137THR00.001-0.0256.018-0.010-0.0100.0000.0000.0000.000
120A138PRO0-0.0290.0062.411-0.845-0.1950.601-0.293-0.9570.003
121A139THR0-0.008-0.0222.383-1.977-0.1601.577-1.251-2.144-0.009
122A140GLY00.000-0.0032.538-1.860-1.5192.416-0.351-2.406-0.010
123A141TRP0-0.003-0.0143.1911.7462.0540.1390.333-0.779-0.002
124A142GLY00.0290.0182.7770.5191.1520.094-0.256-0.4720.000
125A143LEU0-0.013-0.0203.3432.1972.8220.110-0.238-0.497-0.001
126A144PRO0-0.0020.0042.469-4.994-3.3931.055-1.233-1.423-0.015
127A145SER0-0.020-0.0343.878-0.478-0.3960.001-0.013-0.0700.000
128A146ASP-1-0.771-0.8856.767-0.974-0.9740.0000.0000.0000.000
129A147SER0-0.076-0.0339.0560.0920.0920.0000.0000.0000.000
130A148ALA0-0.0340.0007.2950.1360.1360.0000.0000.0000.000
131A149LEU0-0.046-0.0419.290-0.068-0.0680.0000.0000.0000.000
132A150GLY0-0.011-0.0059.4390.0050.0050.0000.0000.0000.000
133A151ILE0-0.045-0.0106.109-0.016-0.0160.0000.0000.0000.000
134A152SER0-0.040-0.0304.8820.0550.0550.0000.0000.0000.000
135A153ASP-1-0.872-0.9256.8180.4720.4720.0000.0000.0000.000
136A154VAL00.0030.0057.631-0.085-0.0850.0000.0000.0000.000
137A155LEU0-0.0180.0205.3350.6720.6720.0000.0000.0000.000
138A156ARG10.8780.9322.400-5.200-4.0221.555-0.934-1.7980.004
139A157GLN00.0300.0012.621-3.080-1.3091.753-0.883-2.640-0.013
140A158VAL0-0.017-0.0062.3410.560-0.6645.600-0.617-3.759-0.003
141A159ASP-1-0.839-0.8873.5540.1670.1770.0130.199-0.2220.000
142A160VAL0-0.003-0.0106.149-0.026-0.0260.0000.0000.0000.000
143A161PRO0-0.013-0.0038.768-0.002-0.0020.0000.0000.0000.000
144A162ILE00.0440.02711.751-0.035-0.0350.0000.0000.0000.000
145A163MET0-0.038-0.00313.1300.0080.0080.0000.0000.0000.000
146A164SER0-0.053-0.06715.822-0.002-0.0020.0000.0000.0000.000
147A165ASN00.018-0.01718.050-0.004-0.0040.0000.0000.0000.000
148A166ALA00.0220.01819.127-0.011-0.0110.0000.0000.0000.000
149A167ASP-1-0.856-0.89918.422-0.104-0.1040.0000.0000.0000.000
150A168CYS0-0.022-0.01311.836-0.057-0.0570.0000.0000.0000.000
151A169ASP-1-0.792-0.90417.461-0.172-0.1720.0000.0000.0000.000
152A170ALA0-0.055-0.01720.371-0.001-0.0010.0000.0000.0000.000
153A171VAL0-0.074-0.02816.8130.0030.0030.0000.0000.0000.000
154A172TYR0-0.086-0.08212.949-0.019-0.0190.0000.0000.0000.000
155A174GLY0-0.027-0.00419.6440.0010.0010.0000.0000.0000.000
156A175ILE0-0.056-0.02717.7130.0080.0080.0000.0000.0000.000
157A176VAL0-0.062-0.02616.891-0.006-0.0060.0000.0000.0000.000
158A177THR0-0.018-0.01319.2870.0220.0220.0000.0000.0000.000
159A178ASP-1-0.897-0.96119.634-0.106-0.1060.0000.0000.0000.000
160A179GLY00.0350.01619.4750.0050.0050.0000.0000.0000.000
161A180ASN0-0.0330.00015.1290.0020.0020.0000.0000.0000.000
162A181ILE00.0070.00912.2600.0270.0270.0000.0000.0000.000
163A183ILE00.0080.0187.3130.0460.0460.0000.0000.0000.000
164A184ASP-1-0.809-0.89410.609-0.207-0.2070.0000.0000.0000.000
165A185SER00.0060.0007.9400.0590.0590.0000.0000.0000.000
166A186THR0-0.026-0.0499.261-0.032-0.0320.0000.0000.0000.000
167A187GLY0-0.067-0.03611.0970.0380.0380.0000.0000.0000.000
168A188GLY00.0120.0198.9290.0430.0430.0000.0000.0000.000
169A188LYS10.7620.8655.3780.1040.1040.0000.0000.0000.000
170A189GLY00.0940.0363.9060.0160.250-0.001-0.056-0.1770.000
171A190THR0-0.093-0.0412.374-3.776-1.1172.677-2.205-3.131-0.013
172A191CYS0-0.027-0.0153.4200.3760.6910.0130.156-0.4830.000
173A192ASN00.000-0.0295.060-0.214-0.101-0.001-0.001-0.1090.000
174A193GLY00.0450.0245.819-0.129-0.1290.0000.0000.0000.000
175A194ASP-1-0.734-0.8762.366-16.323-11.7905.406-4.123-5.816-0.055
176A195SER0-0.020-0.0134.8600.5890.652-0.001-0.005-0.0560.000
177A196GLY00.0340.0067.9200.0410.0410.0000.0000.0000.000
178A197GLY0-0.0140.0065.2080.1210.1210.0000.0000.0000.000
179A198PRO0-0.0300.0015.7530.0480.0480.0000.0000.0000.000
180A199LEU00.0010.0095.8680.0380.0380.0000.0000.0000.000
181A200ASN0-0.010-0.0146.821-0.034-0.0340.0000.0000.0000.000
182A201TYR00.0460.0049.6380.0200.0200.0000.0000.0000.000
183A202ASN0-0.049-0.02712.589-0.008-0.0080.0000.0000.0000.000
184A203GLY00.0230.01714.625-0.009-0.0090.0000.0000.0000.000
185A204LEU0-0.032-0.00714.939-0.009-0.0090.0000.0000.0000.000
186A209THR00.0260.00710.5680.0120.0120.0000.0000.0000.000
187A210TYR00.027-0.00911.846-0.005-0.0050.0000.0000.0000.000
188A211GLY0-0.015-0.01111.160-0.004-0.0040.0000.0000.0000.000
189A212ILE00.0030.0219.2360.0100.0100.0000.0000.0000.000
190A213THR0-0.032-0.0124.7380.0790.142-0.001-0.001-0.0600.000
191A214SER0-0.042-0.0417.699-0.033-0.0330.0000.0000.0000.000
192A215PHE0-0.008-0.02610.692-0.031-0.0310.0000.0000.0000.000
193A216GLY00.1000.04710.147-0.004-0.0040.0000.0000.0000.000
194A217ALA0-0.0020.00711.0990.0330.0330.0000.0000.0000.000
195A217ALA0-0.002-0.01112.539-0.059-0.0590.0000.0000.0000.000
196A218ALA0-0.077-0.03414.6380.0160.0160.0000.0000.0000.000
197A219GLY0-0.0020.00711.4650.0520.0520.0000.0000.0000.000
198A221GLU-1-0.877-0.9498.061-0.498-0.4980.0000.0000.0000.000
199A222ALA0-0.080-0.0379.5460.1340.1340.0000.0000.0000.000
200A223GLY0-0.025-0.00211.1850.0670.0670.0000.0000.0000.000
201A224TYR0-0.024-0.00712.2770.0690.0690.0000.0000.0000.000
202A225PRO00.0130.00811.283-0.063-0.0630.0000.0000.0000.000
203A226ASP-1-0.770-0.8316.848-0.899-0.8990.0000.0000.0000.000
204A227ALA00.010-0.0089.4600.1060.1060.0000.0000.0000.000
205A228PHE00.0260.0035.589-0.077-0.0770.0000.0000.0000.000
206A229THR0-0.019-0.03211.0080.0340.0340.0000.0000.0000.000
207A230ARG10.7670.86313.2780.1090.1090.0000.0000.0000.000
208A231VAL00.0310.01013.3880.0060.0060.0000.0000.0000.000
209A232THR0-0.034-0.06016.0880.0030.0030.0000.0000.0000.000
210A233TYR0-0.042-0.00418.8380.0070.0070.0000.0000.0000.000
211A234PHE0-0.019-0.00917.953-0.001-0.0010.0000.0000.0000.000
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